The Prefix and Suffix does not work the way it should when one is using the RTL language. I've tracked the issue and found that in 960 RTL css files in prefix and suffix section we have: 

/*
 * ==========================================================
 * Prefix
 * ==========================================================
 */
.container-12 .prefix-3 {
  padding-left: 0;
  padding-right: 300px;
}

/*
 * ==========================================================
 * Suffix
 * ==========================================================
 */
.container-12 .suffix-3 {
  padding-right: 0;
  padding-left: 300px;
}

With this css when one applies both 3 column prefix and suffix to make the container narrow, both the suffix and prefix applies to one side on the region (in my case to the left of content region) .
I just removed the padding-right: 0; and padding-left:0; from the RTL css file and now it is working.
Would you please check this solution and see if my workaround is correct?